Simple sequence repeat polymorphism in Quality Protein Maize (QPM) lines

A set of 23 Quality Protein Maize (QPM) lines, including 13 lines developed in India and 10 lines at CIMMYT (International Maize and Wheat Improvement Center), Mexico, was analyzed using microsatellite or simple sequence repeat (SSR) markers. Polymorphic profiles for 36 SSR loci have aided in differentiating the QPM inbred lines. The study resulted in identification of SSR markers, such as bnlg439, phi037, bnlg125, dupssr34 andbnlg105, with high polymorphism information content in the selected QPM genotypes. Detection of 30 unique/rare SSR alleles could contribute to effective differentiation of 14 of the 23 QPM inbreds. An opaque2-specific microsatellite marker, phi057, also facilitated differentiation of opaque2-carrying QPM inbreds from the non-opaque genotypes. Analysis using SSR markers indicated high levels of heterozygosity in majority of the Indian QPM lines and in one CIMMYT QPM inbred, CML188. Cluster analysis using SSR data, followed by canonical discriminant analysis, clearly distinguished the Indian QPM inbreds from those developed at CIMMYT. The cluster patterns were largely in congruence with the available pedigree information of the QPM inbreds studied. The study demonstrates the effectiveness of SSR markers in QPM genotype discrimination and analysis of genetic relationships, and could potentially contribute towards effective utilization of the elite QPM germplasm in Indian maize breeding programmes. This revised version was published online in July 2006 with corrections to the Cover Date.     

线粒体DNA由来的RAPD标记能鉴别水稻雄性不育和可育细胞质

以野败型细胞质的水稻雄性不育系珍汕97A及其保持系珍汕97B的总DNA为模板,从100个引物中筛选到OPA12对珍汕97A能扩增出一条1600 bp的特异带.用OPA12扩增野败型细胞质的龙特浦A及其保持系龙特浦B、矮败型细胞质的协青早A及其保持系协青早B、恢复系明恢63、珍汕97A/明恢63的F1和F2个体的总DNA,不育系、F1和F2所有调查个体都有16     

Present and future of quantitative trait locus analysis in plant breeding

The joint analysis of genotype marker segregation and phenotypic values of individuals or lines enables the detection and location of loci affecting quantitative traits (QTL). The availability of DNA markers and powerful biometric methods has led to considerable progress in QTL mapping in plants. The most obvious applications of QTL analysis seem to be marker‐assisted selection (MAS) in breeding and pre‐breeding and QTL cloning. However, other areas are envisaged where QTL analysis can contribute decisively. These are: the understanding of complex traits such as plant‐pathogen interaction; plant genomics, connecting proteins and regulatory elements of known functions to QTL by candidate gene analysis; and germplasm enhancement through a characterization that allows its efficient utilization. The success in all these applications depends primarily on the reliability and accuracy of the QTL analysis itself. Therefore, the discussion of its limitations will constitute an important part of this review.     

Bulked segregant analysis to detect main effect QTL associated with grain quality parameters in Basmati 370/ASD 16 cross in rice Oryza sativa L) using SSR markers

In the present study a population consisting of 247 F₂ individuals from the cross between Basmati 370, a superior quality basmati variety and ASD16, a non-basmati high-yielding variety was analyzed for their segregation pattern of grain length (GL), grain breadth (GB), cooked grain length (CGL), cooked grain breadth (CGB), and gelatinization temperature (GT). Except GT, all other traits showed normal distribution indicating the polygenic control over the traits. The correlation analysis between traits indicated that GT had positive significant association with GL (0.125), and CGL (0.243). To identify main effect QTL (MQTL) for the above grain quality traits, both the parents were surveyed with 86 primer pairs of simple sequence repeats (SSR). The parental survey revealed 63.95% polymorphism between parents. In order to detect the MQTL associated with grain quality traits, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The number of individuals forming the bulk influenced the identification of putative marker(s) for each of the traits. The association of putative markers identified based on DNA pooling from selected segregants was established by Single Marker Analysis (SMA). The results of SMA revealed that SSR markers, RM225 on chromosome #6 and RM247 on chromosome #12 showed significant association with GB and CGB respectively. It is established that molecular marker analysis involving DNA pooling of phenotypic extremes and selective genotyping helps to detect MQTL for complex traits involving early segregating generations. The molecular marker analysis involving the DNA pooling of phenotypic extremes could be a useful strategy to detect the genetic loci with major effects of other complex grain quality traits in rice.     

The use of AFLP markers for cultivar identification in apricot

Amplified fragment length polymorphism (AFLP) molecular markers were employed for the fingerprinting of 118 accessions of apricot, including cultivated varieties and related apricot species. Five primer combinations were tested and 165 polymorphic bands produced which could uniquely differentiate all accessions under investigation. Primer combinations were rated according to the multiplex ratio, the polymorphic index content and the discrimination power parameters and superior combinations were identified. AFLP markers were used in cluster analysis carried out with the UPGMA and the neighbour‐joining methods and parsimony analysis. Four groups of similar accessions were identified: (i) those from the Mediterranean basin, (ii) from China, (iii) from continental Europe and (iv) mixed Europe‐North America accessions. In the principal component analysis the first three components accounted for 17% of the total variability existing among accessions. Because the most important regions where apricot is cultivated in the world were represented in the analysis, with a large number of varieties, it was possible to discuss the data in the light of current phylogenetic hypotheses on the origin and evolution of the species.     

Cytogenetics of a new trispecies hybrid in cotton: [(Gossypium hirsutum L. × G. thurberi Tod.)2 × G. longicalyx Hutch. & Lee]

A three‐species hybrid named HTL including Gossypium hirsutum L. [2n = 4 x = 52, (AD)₁ genome] was created using the pseudophyletic introgression method with G. longicalyx Hutch. & Lee (2n = 2x = 26, F₁ genome) as donor parent and G. thurberi Tod. (2n = 2x = 26, D₁ genome) as bridge species. The new hybrid was totally self‐sterile and its interspecific status was confirmed using simple sequence repeat markers and cytogenetic analysis. Cytogenetic studies showed that its chromosome configuration was 2n = 52 = 14.13 I + 15.10 II + 1.03 III + 0.9 IV + 0.03 V + 0.13 VI (where I, II, III, IV, V and VI are univalents, bivalents, trivalents, tetravalents, pentavalents and hexavalents, respectively). Prospects for successfully exploiting the HTL hybrid in breeding programmes are discussed.     

Morphological and molecular characterization of Italian emmer wheat accessions

Summary The characterization of 39 Italian ecotypes and cultivars of Triticum turgidum L. spp. dicoccum Shrank ex Schübler (emmer wheat) was performed utilizing agro-morphological and molecular tools. Emmer wheat is a hulled species which grows wild in the Near East and is still cultivated in the Mediterranean Basin. Due to its characteristics, in Italy it is cultivated mainly in marginal lands of central and southern Italy, where local varieties, adapted to the natural environment where they originated, are used. Emmer wheat cultivation has been drastically reduced during the last century as a consequence of its low yield. Nevertheless, more recently, its agronomic and nutritive values, together with its use in health food products, made its cultivation economically viable in the marginal lands with a parallel increase of the cultivated area which is now more than 2000 ha. In the present paper the results of morphological evaluation, carried out in an experimental field in central Italy using a randomized block design with three replications, and molecular characterization are reported. The analysed material showed distinctive molecular traits and the existence of a huge amount of diversity not only between varieties, but also within them. When the accessions were clustered utilizing their genetic distance, the clusters were not always in agreement with the accessions origins. The obtained results gave information that can be useful for: (i) future registration of material, (ii) germplasm conservation and (iii) use of this valuable source of emmer germplasm for future breeding programmes.     

Agronomic performance and molecular assessment of tissue culture-derived barley lines

In order to assess the genetic variability among regenerants. field trials were conducted with 64 barley lines derived from tissue culture (TCD lines) of four Bulgarian barley varieties. The results indicate that the agronomic performance was altered by tissue culture regeneration and the frequency of variation was cultivar dependent. Seven TCD lines showing desirable agronomic characters were selected in the SC1₆ progeny. Molecular markers (protein, restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) have used applied to determine the variability induced by tissue culture. Polymorphism was detected in sequences coding for C-hordeins in line 70 derived from cv.‘Jubiley’Two lines from cv.‘Ruen’exhibited polymorphic bands after hybridization with a mitochondrial DNA probe. RAPD assays have been carried out using 20 different l0-mer primers. Heritable polymorphisms in several TCD lines have been observed.     

Chromosomal location of powdery mildew resistance gene Pm16 in wheat using SSR marker analysis

The use of resistant cultivars is a most economical way to control powdery mildew (Blumeria graminis f.sp. tritici) in wheat (Triticum aestivum L.). Identification of molecular markers closely linked to resistance genes can greatly increase the efficiency of pyramiding resistance genes in wheat cultivars. The objective of this study was to identify molecular markers closely linked lo the powdery mildew resistance gene Pm16. An F₂ population with 156 progeny was produced from the cross‘Chancellor’(susceptible) ב70281’ (resistant), A total of 45 SSR markers on chromosomes 4A and 5B of wheat and 15 SSRs on chromosome 3 of rice was used lo lest the parents, as well as the resistant and susceptible bulks: the resulting polymorphic markers were used to genotype the F₂ progeny. Results indicated that the SSR marker Xgwm159, located on the short arm of chromosome 5B, is closely linked to Pm16 (genetic distance: 5.3 CM). The cytogenetical data presented in an original report, in combination with this molecular analysis, suggests that Pm16 may he located on a translocated 4A.5BS chromosome.     

Induced mutations – A new paradigm in plant breeding

The use of ionizing radiation, such as X-rays, gamma rays and neutrons and chemical mutagens for inducing variation, is well established. Induced mutations have been used to improve major crops such as wheat, rice, barley,cotton, peanuts, and beans, which are seed propagated. Since the establishment of the Joint FAO/IAEA Division of the Nuclear Techniques in Agriculture, more than 1800 cultivars obtained either as direct mutants or derived from their crosses have been released worldwide in 50 countries. In vegetatively propagated plants, many of mutants were derived from irradiating rooted stem cuttings, detached leaves, and dormant plants. According to the FAO/IAEA database, of the 465 mutants released among the vegetatively propagated plants, most are in the floricultural plants and a few in fruit trees. These include chrysanthemum, Alstroemeria, dahlia, bougainvillea, rose, Achimenes,begonia, carnation, Streptocarpus, and azalea. The irradiation of in vitro cultured date palm, apple, potato, sweet potato and pineapple now provides a means to treat large populations which would not have been possible before. Irradiation of micropropagated plants, axillary and adventitious buds, apical meristems, regenerative callus cultures, anthers and microspores, and somatic embryos provides a miniaturized version of trees and seeds in the Petridish instead of the field. During the last decade, the use of radio-actively labeled probes in recombinant DNA research for cloning and mapping plant genes and transgenesis, particularly for RFLP, micro satellite based DNA fingerprinting, has become a routine procedure. Many homeotic mutants that change floral development have been isolated in Arabidopsis, Petunia, Antirrhinum and Lycopersicon. Mutants of Arabidopsis are being used to analyze genes, which determine response to auxins, cytokinins, gibberellin, abscisic acid and ethylene in plant growth, floral development and senescence, fruit formation and ripening. These mutants are facilitating the isolation, identification and cloning of the genes, which would ultimately help in designing crops with improved yield, increased stress tolerance, longer shelf-life and reduced agronomic inputs. The identification and analysis of mutants by using molecular techniques of DNA fingerprinting and mapping with PCR based markers, such as RAPDs, AFLP and STMS, and mutant tagging shall bring a new dimension in gene technology. Already, mutations can be linked to changes in DNA sequences for some plant traits and to establish molecular maps in structural and functional genomics of crop plants. These in turn would lead to a rapid enhancement of crop yields and quality. This revised version was published online in July 2006 with corrections to the Cover Date.